The album introduces us to Coheed and his wife Cambria. Coheed is infected with a serum that will grant him the power to destroy the universe if activated.

Sanchez's website, www.evilinkcomics.net, sums up the story of this part:

Man and wife Coheed and Cambria are used as the centerpiece to enable Supreme Tri-Mage Wilhelm Ryan's attempt at destroying his archrival Mage, Mariah Antillarea. Due to a memory swiping years ago, the couple are led to believe that their former lives have now come back to haunt them. They’re told by General Mayo Deftinwolf (Ryan's Right hand) that they were long ago implanted with a great threat to Heaven’s Fence, The Monstar Virus. A virus with the ability to turn its host (Coheed) into a being powerful enough to drain the Keywork's energy sources to spark Armageddon, while their dear old counterpart, Inferno was given the only means to unlock it. Through more lies, they are led to believe their children have genetically acquired a mutated form of the virus, the Sinstar. This new strain only requires its host to mature to a certain age, and has no antidote unlike the Monstar. Their children cannot be saved and time will not side with them. Coheed and Cambria are faced with an unimaginable dilemma: to murder their own children or face Armageddon.

Trivia

The brief sound clip at the beginning of Junesong Provision (Acoustic Demo) (re-release only) is a famous line from cult classic Sam Raimi film Army of Darkness, in which Bruce Campbell refers to his shotgun as his "boomstick."

The hidden track "IRO-Bot" is placed at the end of the demo version of "Everything Evil" on the 2005 re-release, instead of the end of "God Send Conspirator". The end of "21:13" found on In Keeping Secrets of Silent Earth: 3 is a reprise of this song. "21:13" also reprises the opening riff of "Time Consumer".